writeToFile            package:arrayMagic            R Documentation

_W_r_i_t_e_s _a _t_e_x_t_u_a_l _r_e_p_r_e_s_e_n_t_a_t_i_o_n _o_f _a_n _e_x_p_r_S_e_t_R_G
_a_n_d/_o_r _a_r_r_a_y_D_a_t_a _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     'writeToFile' generates a well-formated tab-deliminated output
     file of data stored in the 'exprSetRG' and/or 'arrayData' objects.
     Different "views" on either a corresponding pair of an
     'exprSetRG'- and an 'arrayData'-object or of a single object
     itself are possible. The argument 'channels' allows to specify the
     "views". The microarray slide or channel annotation, as well as
     the spot annotation is aligned to the data block if given. For
     further restriction and control of the output, e.g. slide subsets
     or ordering of slides, you may use the subsetting operations
     offered by the 'exprSetRG-class' and 'arrayData-class' beforehand
     (e.g. slideSubset and [] ).

_U_s_a_g_e:

     writeToFile(arrayDataObject, exprSetRGObject, additionalDataMatrix, rowSelection, slideNameColumn, channels=c("logRatio"), fileName="dumpedData.txt", savePath=".", fullOutput=TRUE, coding=FALSE)

_A_r_g_u_m_e_n_t_s:

arrayDataObject: object of class 'arrayData'; optional/required, cf.
          'channels'; default: missing

exprSetRGObject: object of class 'exprSetRG'; optional/required, cf.
          'channels'; default: missing

additionalDataMatrix: class 'matrix'; optional; default: missing. The
          rows must correspond to those of the data objects; 'colnames'
          must be supplied.

rowSelection: vector of indexes; optional; default: missing

slideNameColumn: character string; optional; default: missing; must
          refer to a valid column in 'getHybAttr'('arrayDataObject') or
          in 'pDataSlide'('exprSetRGobject') 

channels: vector of character strings; default: 'c("logRatio")'; valid
          character strings are: "logRatio", "green", "red",
          "rawGreen", "rawRed", "rawGreenRelative", "rawRedRelative",
          "se.exprsLogRatio", "se.exprsGreen", "se.exprsRed".
          "Raw"-types must not mix with not "raw"-types and vice versa.
          "logRatio"-types must not mix with "colour"-types. The "raw"
          types require the argument 'arrayDataObject', all other types
          requires at least the argument 'exprSetRGObject'.

fileName: character string; required; default: "dumpedData.txt"

savePath: character string; required; default: "."

fullOutput: logical; adds 'phenoData' information at the top of the
          table ; by default: 'TRUE'

  coding: logical; adds integer-coded-'phenoData' information at the
          top to the table only if 'coding = TRUE' and 'fullOutput =
          TRUE'; default: 'FALSE'

_D_e_t_a_i_l_s:

_V_a_l_u_e:

     The function is called for its side effect, i.e. writing a file.

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'exprSetRG-class', 'arrayData-class', 'write.htmltable'

_E_x_a_m_p_l_e_s:

       
      

